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Bio-Rad Laboratories, Inc. Omnition Single-Cell Analysis Software

This analysis pipeline is designed to analyze single-cell ATAC-Seq data and combinatorial single-cell ATAC-Seq data. The pipeline is built using a combination of Nextflow, Conda environments, and Docker containers. To accommodate user environments, the pipeline containers are also compatible with Singularity.

Dependencies

  • This software has been tested on the following Linux operating systems: 64-bit CentOS 7 and 8, and Ubuntu 18.04.6, 20.04 LTS, 21.04, and 21.10.
    • The software may run on additional Linux distrubitions and/or versions beyond these if they are able to run the dependencies and versions listed below, but these are not officially supported.
  • Internet connection
  • Nextflow (21.04.0-22.10.3)
  • Docker (>=20.10.7) or Singularity (>=3.6.4)

NOTE: If using Docker, your USER must be added to the docker root user group before executing the pipeline. On shared systems, such as HPC clusters, this may not be possible due to security risks and the pipeline should be executed using the Singularity profile (default) instead.

NOTE: The user must verify with their system administrator that Docker or Singularity is available before using Omnition.

Quick Start

Configure Parameters

The pipeline requires a YAML- or JSON-formatted file listing assay-specific parameters when not running the test data. A detailed description of the file contents, including the structure, are provided below. Assay parameters must be nested under the appropriate assay name (atac) using indentation and only one value may be listed per line. File paths must be relative to the directory where the analysis is being executed. If specifying multiple files, you must create a new nested level of parameters. See below for an example of how to nest parameters as part of a mixed species analysis.

Parameters

NOTE: When configuring bead and cell calling settings, priority will be as follows:

  1. Sample-specific settings within an assay-specific section
  2. Assay-specific settings
  3. Global settings
  4. Default settings

Global

  • outputDir (default: "./results"): Location to deposit final results and reports.

ATAC

  • workflow: Type of workflow to be executed. Must be "reference", "analysis", or "full".

    • "reference": Only perform the reference-generation portion of the given assay
      • Required parameters:
        • reference
          • directory
          • fasta
          • gtf
      • Optional parameters:
        • blocklist
        • mixed
        • barcodedTn5
        • tssWindowSize
    • "analysis": Only perform the analysis portion of the given assay
      • Required parameters:
        • input
        • reference
        • blocklist
      • Optional parameters:
        • mitoContig
        • mixed
        • barcodedTn5
        • ti
        • barcodedTn5Config
        • i7asti
        • tiread
        • tssWindowSize
        • mergeMethod
        • qualityThreshold
        • barcode
          • force
        • trim
        • sortSize
        • rounding
        • maxInsertSize
        • tierroroverride
        • overrides
      • NOTE: This workflow assumes that references have already been generated and will error if they are not found.
    • "full": Perform both reference-generation and analysis portions of the given assay
      • Required parameters:
        • reference
          • directory
          • fasta
          • gtf
        • input
        • blocklist
      • Optional parameters:
        • mitoContig
        • mixed
        • barcodedTn5
        • ti
        • barcodedTn5Config
        • i7asti
        • tiread
        • tssWindowSize
        • mergeMethod
        • qualityThreshold
        • barcode
          • force
        • trim
        • sortSize
        • maxInsertSize
        • tierroroverride
        • overrides
  • reference:

    • directory: Directory path to write newly-generated reference files to and/or containing pre-generated references.
      • Required.
      • Must be quoted.
    • fasta: File path(s) to reference FASTA file(s).
      • Required.
      • Optionally gzip compressed; must be quoted.
    • gtf: File path(s) to reference GTF file(s).
      • Required.
      • Optionally gzip compressed; must be quoted.
    • blocklist: File path(s) to reference blocklist BED file(s).
      • Optional. Must be quoted.
  • input: Directory path containing raw FASTQ files.

    • Required.
    • Must be gzip compressed; must be quoted.
  • mitoContig: The name of the mitochondrial contig in the reference.

    • Optional.
    • DEFAULT: "MT".
  • mixed: Boolean value indicating if the mixed species workflow should be used.

    • Optional.
    • If false: Only allows a single FASTA and GTF file to be provided for reference workflow.
    • If true: Requires two FASTA and GTF files to be provided for reference workflow.
    • DEFAULT: false.
  • barcodedTn5: Boolean value indicating if the samples have tagmentation indexes.

    • Optional.
    • If false: Samples are assumed to not have tagmentation indexes.
    • If true: All samples are assumed to have tagmentation indexes and read 2 is parsed for the index. Index reports are generated.
    • DEFAULT: false.
  • ti: A list of user defined TI sequences.

    • Optional.
    • See ATAC Combinatorial Config file below for example of formatting.
    • DEFAULT: Presets are present in conf/atac_preset.config.
  • barcodedTn5Config: File path to a CSV file that specifies the TIs and FASTQs assigned to each sample.

    • Optional.
    • DEFAULT: None.
    • If barcodedTn5 is set to true, and no config file is provided, the default behavior is to merge all TIs and FASTQs as a single sample. Only include TIs present in a given experiment as unused TIs that are included in the config can lead to errors. Must be formatted with these three columns:
    • Sample The name of the sample.
    • Fastq The name given to the fastq file pair.
    • TI: The name of the TI used (see conf/atac_preset.config for list of preset TIs).
  • i7asti: Boolean value indicating whether the I7 index should be treated as a tagmentation index.

    • Optional.
    • Requires barcodedTn5 to be true.
    • DEFAULT: false.
  • tiread: The read that contains the TI sequence, assuming the TI is not in the i7 sequence.

    • Optional.
    • Requires barcodedTn5 to be true and i7asti to be false.
    • One of "r1" or "r2".
    • DEFAULT: "r1".
  • tssWindowSize: The full window size in bases around TSS for TSS enrichment score calculations.

    • Optional.
    • Must be an even integer greater than 0.
    • DEFAULT: 4000.
  • mergeMethod: The read(s) in a pair to use for determining the transposase insertion site used in bead merging.

    • Optional.
    • One of "r1", "r2", or "both".
    • DEFAULT: "both".
  • qualityThreshold: Minimum MAPQ for a read to be included in the analysis.

    • Optional.
    • DEFAULT: 30.
  • barcode: Settings related to knee calling configuration.

    • Optional.
    • force: The number of barcodes to return. This will bypass all knee calling algorithms and return the top n number of barcodes based on unique reads.
      • An integer greater than zero.
      • DEFAULT: None. Omnition will determine the number of cells in each sample.
  • trim: Number of bases to trim from the 5' end of R2 read.

    • Optional.
    • An integer greater than or equal to 0.
    • DEFAULT: 0.
  • sortSize: Set the sort collection size ratio for MarkDuplicates.

    • Optional.
    • A floating point number greater than 0.
    • This parameter is to be used when the module runs out of memory due to very high duplication rate.
    • Lower the number to make memory footprint size more manageable. Recommended trial value is 0.01 in case of memory errors.
    • DEFAULT: 0.25.
  • rounding: Rounds insert sites to the nearest 10, 100, or 1000 bases before performing bead merging.

    • Optional.
    • One of 10, 100, or 1000.
    • DEFAULT: 0; no rounding is performed.
  • maxInsertSize: The largest insert that Omnition will recognize.

    • Optional.
    • An integer greater than 100.
    • DEFAULT: 2000.
  • tierroroverride: Boolean value.

    • If set to true, the pipeline will ignore errors in the TI configuration file. Only fastq-TI combinations specified in the config file will be used. All others observed in the sequencing data will be ignored.
    • DEFAULT: false.
  • overrides: (non-combinatorial) Sample-specific settings for overriding barcode calling and bead merging configuration.

    • <sample_id>: The sample_id of the sample to be overriden.
      • barcode: See above for description.
        • force
      • trim: See above for description.
      • mergeMethod: See above for description.
  • overrides: (combinatorial) FASTQ+TI-specific settings for overriding barcode calling and deconvoulution configuration. Overrides can be set on the FASTQ level or on the FASTQ+TI level. Overrides set on the FASTQ level will be applied to all FASTQ+TI combinations coming from that FASTQ file.

    • <sample_id>: The FASTQ name of the fastq to be overriden.
      • barcode: See above for description.
        • force
      • trim: See above for description.
      • mergeMethod: See above for description. Example: If the FASTQ files were named SampleA_S1_R1_001.fastq.gz and SampleA_S1_R1_001.fastq.gz, the FASTQ name would be SampleA_S1.
    • <sample_id>: The FASTQ name of the fastq to be overriden.
      • <TI_name>: The TI name of the TI to be overriden. Example: TI12.
        • barcode: See above for description.
          • force
        • trim: See above for description.
        • mergeMethod: See above for description.

Examples

parameters_atac.yaml (ATAC-Seq)

atac:
  workflow: "full"
  input: "test/data/atac/normal/"
  reference: 
    directory: "test/references/atac/"
    fasta:
        species1: "test/references/atac/final_hg38.fa.gz"
        species2: "test/references/atac/final_mm10.fa.gz"
    gtf:
        species1: "test/references/atac/final_hg38.gtf.gz"
        species2: "test/references/atac/final_mm10.gtf.gz"
  mixed: true 

parameters_catac.yaml (Combinatorial ATAC-Seq Superloading)

atac:
  workflow: "full"
  input: "test/data/atac/combinatorial/"
  reference: 
    directory:"test/references/atac/"
    fasta:
        species1: "test/references/atac/final_hg38.fa.gz"
        species2: "test/references/atac/final_mm10.fa.gz"
    gtf:
        species1: "test/references/atac/final_hg38.gtf.gz"
        species2: "test/references/atac/final_mm10.gtf.gz"
  mixed: true
  barcodedTn5: true
  ti:
    ti1: "AAAGAA"
    ti2: "TTTGGG"
  barcodedTn5Config: "test/config/atac/atac_mixed_TIs.csv"
  tiread: "r1"

NOTE: Removing the barcodedTn5Config parameter from above will change the configuration to Combinatorial ATAC-Seq Superloading.

atac_mixed_TIs.csv

Sample,Fastq,TI
SampleA,Cycler_S3_newindex,mycustomti1
SampleB,Cycler_S3_newindex,mycustomt12

Custom Transposition Index (TI) definition for combinatorial ATAC-Seq

To use custom TIs, add the TI sequences to your yaml config file. See parameters_catac.yaml, above, for an example.

Custom TIs must be of equal length and must be located in one of the following locations:

  • The 5' end of R2 (see parameter tiread: r2)
  • Immediately after the bead barcode in R1 (set parameter tiread: r1)
  • In the i7 sequencing barcode (see parameter i7asti: true).

For TIs located in the 5' end of R2, use the trim parameter to remove all bases upstream of the TI sequence.

References

Omnition is compatible with Human/GRCh38 and Mouse/GRCm39 references from ENSEMBL. It is not compatible with other species or references produced by NCBI.

Execution

The pipeline may be executed using either Singularity (default) or Docker. Upon execution, Nextflow will download the pipeline from GitHub. The code may be found in ~/.nextflow/assets/BioRadOpenSource/omnition/ after download. Omnition will download the Singularity images or Docker containers as needed.

Please note the use of single - and double -- in the execution commands. Arguments with a single - in front are Nextflow arguments and those with double -- are user-defined parameters.

NOTE: Nextflow gives each pipeline run a randomly generated name formatted as [adjective_name]. Names are taken from those listed in the following code (https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy). These run names are generated by Nextflow and not endorsed by Bio-Rad.

After completion, reports can be found in the report/ subdirectory and intermediate files can be found in the Sample_Files/ subdirectory. Additionally, a Nextflow cache directory (.nextflow/) and working directory (work/) will be created in the directory where Nextflow was executed.

Nextflow Functionality

Resuming an Analysis

Interrupted or failed analyses can be restarted from their stopping point by using the -resume flag in the pipeline execution commands. Deleting the cache (.nextflow/) or working directory (work/) will clear the cache and disable the -resume functionality.

Diagnostics

Pipeline diagnostic reports generated by Nextflow will be produced by default by Omnition. For each analysis, a pipeline_info directory will be generated in the --outputDir and populated with a Nextflow execution report, trace report, and timeline report. For more information on these reports, see the Nextflow documentation.

Singularity

nextflow run BioRadOpenSource/omnition -params-file <path to parameters.yaml> --outputDir <output directory path>

Docker

nextflow run BioRadOpenSource/omnition -params-file <path to parameters.yaml> --outputDir <output directory path> -profile docker

Test Data

There are two test profiles available to run with the pipeline. The profile demo_atac runs with the settings specified in parameters_atac.yaml, above. The profile demo_catac runs with the settings specified in the parameters_catac.yaml example, above. The parameters used in these different testing profiles can be found in conf/test.config.

Below are examples of how to run the different testing profiles while executing the pipeline with Docker (-profile docker) or Singularity (-profile standard). The test type is then specified separated by a comma in the -profile flag.

Docker:

nextflow run BioRadOpenSource/omnition --outputDir <output directory path> -profile docker,demo_atac
nextflow run BioRadOpenSource/omnition --outputDir <output directory path> -profile docker,demo_catac

Singularity:

nextflow run BioRadOpenSource/omnition --outputDir <output directory path> -profile standard,demo_atac
nextflow run BioRadOpenSource/omnition --outputDir <output directory path> -profile standard,demo_catac

Appendix

Resource Allocation

Omnition is composed of a series of “processes” that connect to form a pipeline. Each process is allocated a portion of the host system’s CPU and RAM when Nextflow’s scheduler launches a processing task. Nextflow’s scheduler launches processes in parallel when the system’s capacity permits it.

Bio-Rad has provided default resource allocations for the processes in Omnition to optimize performance on a system with 16 CPU and 64 GB RAM. If a process fails due to insufficient resources, it will be retried a maximum of two times with each retry requesting double the resources of the previous one. Should the process fail after a second retry, no further retries will be carried out. Each process is assigned two labels that dictate the CPU and memory allocation to that process. The default labels are defined in the tables below.

CPU Allocation Labels

Label CPUs
cpu_xsmall 1
cpu_small 2
cpu_medium 4
cpu_large 8
cpu_xlarge 16

Memory Allocation Labels

Label RAM (GB)
memory_xxsmall 0.9375
memory_xsmall 3.75
memory_small 7.5
memory_medium 15
memory_large 30
memory_xlarge 60

Default Process Labels

Process CPUs RAM
AGGREGATE_METRICS cpu_small memory_xsmall
ANNOTATE_FRAGMENTS cpu_medium memory_medium
ARCHR cpu_small memory_xlarge
ARCHR_REFERENCE cpu_small memory_large
ASSEMBLE_BASIC_QC cpu_medium memory_xxsmall
ASSEMBLE_FRAGMENTS cpu_xsmall memory_xsmall
BEAD_FILT_SUMMARY cpu_small memory_xxsmall
BUILD_REPORT_CONTENTS cpu_medium memory_xxsmall
BWA_ALIGNMENT cpu_xlarge memory_xlarge
BWA_INDEX cpu_small memory_large
CALCULATE_BEADS_PER_DROP cpu_xsmall memory_xxsmall
CALCULATE_INSERT_SIZE_METRICS cpu_small memory_xsmall
CALL_PEAKS cpu_xsmall memory_medium
CHECK_MITO_CONTIG cpu_xsmall memory_xsmall
CHECK_TI_COUNTS cpu_xsmall memory_xxsmall
CHECK_TI_COUNTS_SUPERLOADED cpu_xsmall memory_xxsmall
CLEAN_PEAKS cpu_xsmall memory_xsmall
COMBINE_BLOCKLISTS cpu_xsmall memory_xxsmall
COMBINE_REFERENCES cpu_small memory_xxsmall
COMPILE_ALIGNMENTS cpu_large memory_xsmall
COMPILE_FRAGMENTS cpu_large memory_medium
COMPILE_QC_STATS cpu_large memory_xxsmall
COMPUTE_DECONVOLUTION_STAT_CHR cpu_medium memory_medium
COMPUTE_TSS_MATRIX cpu_small memory_xxsmall
CUTADAPT_HEADCROP cpu_medium memory_medium
DEAD cpu_small memory_xxsmall
DETERMINE_BARCODE_ALLOWLIST cpu_medium memory_small
DETERMINE_BARCODE_MERGES cpu_medium memory_small
FASTQC cpu_small memory_small
FILTER_BLOCKLISTS cpu_xsmall memory_xxsmall
FILTER_REFERENCES cpu_xsmall memory_xxsmall
FINAL_BAM_MERGE cpu_xlarge memory_xxsmall
FINAL_FRAG_MERGE cpu_medium memory_xsmall
FINAL_QC_SE cpu_medium memory_xlarge
FORMAT_BLOCKLIST cpu_xsmall memory_xxsmall
FRACTION_OF_READS_IN_PEAKS cpu_xsmall memory_xsmall
FRACTION_OF_READS_IN_TSS cpu_xsmall memory_xsmall
GENERATE_EMPTY_BLOCKLIST cpu_xsmall memory_xxsmall
GENERATE_GENOME_SIZES cpu_medium memory_xxsmall
GENERATE_REPORT cpu_small memory_small
GENERATE_TSS_WINDOWS cpu_medium memory_xxsmall
GUNZIP cpu_xsmall memory_xxsmall
MAKE_COUNT_MATRIX cpu_xsmall memory_xlarge
MARK_DUPLICATES cpu_medium memory_xlarge
MERGE_LANES cpu_xsmall memory_xxsmall
MERGE_REANN_READ_COUNTS cpu_small memory_xxsmall
PUBLISH_PARAMETERS cpu_medium memory_xxsmall
REANNOTATE_BAM cpu_medium memory_xxsmall
REANNOTATE_FRAGMENTS cpu_medium memory_medium
SEQUENCE_SATURATION cpu_medium memory_medium
SPLIT_BAM cpu_xlarge memory_xsmall
SPLIT_FASTQ cpu_xsmall memory_xxsmall
SUMMARIZE_ALIGNMENTS cpu_medium memory_xsmall
SUMMARIZE_MIXED_SPECIES cpu_xsmall memory_xxsmall
TAG_BARCODES cpu_xlarge memory_xlarge
TI_DEAD_CONFIG cpu_xsmall memory_xxsmall
TI_ERROR_CHECK cpu_xsmall memory_xxsmall
TI_WARNING_MESSAGES cpu_xsmall memory_xsmall
TSS_ENRICHMENT cpu_xsmall memory_xxsmall
VALIDATE_TI_CONFIG cpu_xsmall memory_xxsmall

Adjusting Resource Allocation

To change the resource allocation for a given resource tier (e.g., increase memory for the memory_xlarge label), create a configuration file like the one below and save it as resources.config:

process{ 
    withLabel: memory_xlarge {  
        memory = 128.GB  
        time = 24.h  
    }
} 

This file should then be saved and passed to Omnition when running the software, for example:

nextflow run BioRadOpenSource/omnition -params-file analysis.yaml -profile standard –c resources.config

The resource allocations in resources.config will then override the default settings.

ATAC BAM File Tags

This pipeline places a number of tags on the bam files produced in the workflow. Below is a table defining them.

Tag Type First Annotated Description
AS i process BWA_ALIGNMENT Assigned by BWA and conforms to SAM specifications: Alignment score from the aligner. Lay definition: See previous sentence.
NM i process BWA_ALIGNMENT Assigned by BWA. The edit distance in the alignment.
MC Z process BWA_ALIGNMENT Compressed representation of the alignment's mate in the [CIGAR format].(https://www.drive5.com/usearch/manual/cigar.html)
MD Z process BWA_ALIGNMENT Mismatching positions and bases.
XS i process BWA_ALIGNMENT Alignment scores for suboptimal alignments.
XA Z process BWA_ALIGNMENT Suboptimal alignment hits. Format: (chr,pos,CIGAR,NM).
XB Z process BWA_ALIGNMENT The bead barcode sequence for a read.
PG Z process MARK_DUPLICATES Indicates MarkDuplicates was executed.
DI i process MARK_DUPLICATES The duplicate set index as assigned by MarkDuplicates.
DB Z process REANNOTATE_BAM The cell barcode.

Blocklist

NOTE: Bio-Rad has adopted the term "blocklist” as a replacement for “blacklist.”

The ATAC analysis workflow will ignore alignments to blocklisted regions within the genome during bead merging. Bio-Rad does not provide blocklists. File name must be in the format SPECIESNAME.blocklist.bed where SPECIESNAME is the same species name used for the fasta and gtf files. Blocklists must be formatted as a three column BED file with feature names matching those in the reference genome FASTA and reference GTF:

chr10      0       45700
chr10      38481300        38596500
chr10      38782600        38967900
chr10      39901300        41712900
chr10      41838900        42107300
chr10      42279400        42322500
chr10      126946300       126953400
chr10      133625800       133797400

A blocklist is not required for the pipeline to execute. If one is not provided, an empty one is generated at runtime.

When doing a mixed species run, up to two blocklists may be supplied.

Publicly available blocklists are available here. The feature names need to be updated to match those of the reference being used.

Benchmarks

The dataset used for quantification was a mixed species run with 1,262,814,294 total paired reads which were downsampled to 4 different levels (100%, 75%, 50%, 25%, 10%) when run through the analysis workflow. Without downsampling the pipeline called 32,812 total cells.

A system with 16 CPUs (Intel Xeon Cascade Lake) and 128 GB RAM was (AWS r5d.4xlarge) used for the runs used to generate these results.

Reference workflow

name realtime (run time) peak_rss (peak RAM usage)
ARCHR_REFERENCE 9m 2s 11.3 GB
BWA_INDEX 2h 25s 8.2 GB
COMBINE_REFERENCES 24s 41.5 MB
FILTER_BLOCKLISTS 18.5s 66.7 MB
FILTER_REFERENCES 26.3s 63.8 MB
FORMAT_BLOCKLIST 4s 57.3 MB
GENERATE_GENOME_SIZES 23.1s 31.2 MB
GENERATE_TSS_WINDOWS 9.8s 137.6 MB
GUNZIP_FASTA 27.2s 58.4 MB
GUNZIP_GTF 9.3s 59.1 MB

Analysis workflow

% of sample reads used total paired reads
100 1,262,814,294
75 947,110,720
50 631,407,146
25 315,703,572
10 126,281,428
name realtime (run time) peak_rss (peak RAM usage) % of initial sample reads used
AGGREGATE_METRICS 3m 12s 767.2 MB 100
AGGREGATE_METRICS 2m 47s 759.1 MB 75
AGGREGATE_METRICS 2m 6s 706.3 MB 50
AGGREGATE_METRICS 1m 39s 643.3 MB 25
AGGREGATE_METRICS 2m 29s 932.1 MB 10
ANNOTATE_FRAGMENTS 9s 957.4 MB 100
ANNOTATE_FRAGMENTS 9s 996.6 MB 75
ANNOTATE_FRAGMENTS 9s 982.8 MB 50
ANNOTATE_FRAGMENTS 9s 650.1 MB 25
ANNOTATE_FRAGMENTS 7s 353.3 MB 10
ARCHR 1h 51m 47s 68.4 GB 100
ARCHR 1h 50m 11s 61.2 GB 75
ARCHR 1h 42m 24s 76.3 GB 50
ARCHR 1h 31m 43s 70.1 GB 25
ARCHR 1h 25m 14s 51.1 GB 10
ASSEMBLE_BASIC_QC 4s 352 MB 100
ASSEMBLE_BASIC_QC 4s 359.7 MB 75
ASSEMBLE_BASIC_QC 4s 351.9 MB 50
ASSEMBLE_BASIC_QC 4s 360.4 MB 25
ASSEMBLE_BASIC_QC 4s 361.9 MB 10
ASSEMBLE_FRAGMENTS 9s 998 MB 100
ASSEMBLE_FRAGMENTS 9s 989.6 MB 75
ASSEMBLE_FRAGMENTS 9s 99.1 MB 50
ASSEMBLE_FRAGMENTS 9s 99.8 MB 25
ASSEMBLE_FRAGMENTS 8s 98.9 MB 10
BEAD_FILT_SUMMARY 11.4s 14.8 MB 100
BEAD_FILT_SUMMARY 9.1s 14.6 MB 75
BEAD_FILT_SUMMARY 6.3s 14.5 MB 50
BEAD_FILT_SUMMARY 3.2s 14.6 MB 25
BEAD_FILT_SUMMARY 2.4s 14.7 MB 10
BUILD_REPORT_CONTENTS 2.5s 122.4 MB 100
BUILD_REPORT_CONTENTS 2.6s 121.9 MB 75
BUILD_REPORT_CONTENTS 2.5s 123.2 MB 50
BUILD_REPORT_CONTENTS 2.5s 122.4 MB 25
BUILD_REPORT_CONTENTS 2.6s 121.8 MB 10
BWA_ALIGNMENT 38m 22s 29.6 GB 100
BWA_ALIGNMENT 43m 50s 29.6 GB 75
BWA_ALIGNMENT 9m 54s 29.2 GB 50
BWA_ALIGNMENT 9m 44s 23 GB 25
BWA_ALIGNMENT 33m 19s 16.5 GB 10
CALCULATE_BEADS_PER_DROP 2s 37.3 MB 100
CALCULATE_BEADS_PER_DROP 2s 36.3 MB 75
CALCULATE_BEADS_PER_DROP 2s 36.4 MB 50
CALCULATE_BEADS_PER_DROP 2s 35.5 MB 25
CALCULATE_BEADS_PER_DROP 3s 74.8 MB 10
CALCULATE_INSERT_SIZE_METRICS 25m 58s 1.1 GB 100
CALCULATE_INSERT_SIZE_METRICS 20m 8s 1.1 GB 75
CALCULATE_INSERT_SIZE_METRICS 13m 54s 972.2 MB 50
CALCULATE_INSERT_SIZE_METRICS 8m 29s 667.4 MB 25
CALCULATE_INSERT_SIZE_METRICS 4m 5s 1.4 GB 10
CALL_PEAKS 44m 6s 3.3 GB 100
CALL_PEAKS 37m 25s 2.7 GB 75
CALL_PEAKS 29m 26s 2.2 GB 50
CALL_PEAKS 17m 51s 1.4 GB 25
CALL_PEAKS 9m 9s 736.3 MB 10
CHECK_TI_COUNTS_SUPERLOADED 41m 20s 14.8 MB 100
CHECK_TI_COUNTS_SUPERLOADED 32m 12s 28 MB 75
CHECK_TI_COUNTS_SUPERLOADED 21m 27s 33.4 MB 50
CHECK_TI_COUNTS_SUPERLOADED 10m 35s 32.6 MB 25
CHECK_TI_COUNTS_SUPERLOADED 1m 57s 14.9 MB 10
CLEAN_PEAKS 13.1s 372.7 MB 100
CLEAN_PEAKS 12.4s 415.2 MB 75
CLEAN_PEAKS 12s 409.5 MB 50
CLEAN_PEAKS 10.8s 372.9 MB 25
CLEAN_PEAKS 9.5s 355.7 MB 10
COMPILE_ALIGNMENTS 2h 11m 50s 403.7 MB 100
COMPILE_ALIGNMENTS 1h 56m 13s 435.4 MB 75
COMPILE_ALIGNMENTS 1h 26m 7s 419.7 MB 50
COMPILE_ALIGNMENTS 50m 8s 385.8 MB 25
COMPILE_ALIGNMENTS 18m 34s 630.5 MB 10
COMPILE_QC_STATS 1.1s 13.1 MB 100
COMPILE_QC_STATS 1.1s 11.8 MB 75
COMPILE_QC_STATS 1s 12 MB 50
COMPILE_QC_STATS 1.4s 12.4 MB 25
COMPILE_QC_STATS 958ms 12 MB 10
COMPUTE_DECONVOLUTION_STAT_CHR 9s 996.6 MB 100
COMPUTE_DECONVOLUTION_STAT_CHR 9s 99.5 MB 75
COMPUTE_DECONVOLUTION_STAT_CHR 9s 99.9 MB 50
COMPUTE_DECONVOLUTION_STAT_CHR 9s 99.6 MB 25
COMPUTE_DECONVOLUTION_STAT_CHR 9.9s 99.9 MB 10
COMPUTE_TSS_MATRIX 1h 56s 1.7 GB 100
COMPUTE_TSS_MATRIX 51m 54s 1.5 GB 75
COMPUTE_TSS_MATRIX 44m 37s 1.2 GB 50
COMPUTE_TSS_MATRIX 34m 42s 802.5 MB 25
COMPUTE_TSS_MATRIX 26m 26s 653.2 MB 10
COUNT_BEADS_PER_PARTITION 3.8s 98.5 MB 100
COUNT_BEADS_PER_PARTITION 7.6s 98.3 MB 75
COUNT_BEADS_PER_PARTITION 6s 98 MB 50
COUNT_BEADS_PER_PARTITION 7.1s 99.7 MB 25
COUNT_BEADS_PER_PARTITION 5.6s 98.6 MB 10
CUTADAPT_HEADCROP 8m 31s 4.3 GB 100
CUTADAPT_HEADCROP 7m 49s 4.1 GB 75
CUTADAPT_HEADCROP 5m 10s 4 GB 50
CUTADAPT_HEADCROP 2m 5s 3.3 GB 25
CUTADAPT_HEADCROP 36.7s 991.6 MB 10
DEAD 3h 31m 53s 135.7 MB 100
DEAD 2h 35m 53s 135.6 MB 75
DEAD 1h 43m 36s 135.7 MB 50
DEAD 51m 51s 135.6 MB 25
DEAD 12m 42s 135.7 MB 10
DETERMINE_BARCODE_ALLOWLIST 3m 5s 1.2 GB 100
DETERMINE_BARCODE_ALLOWLIST 2m 13s 1.2 GB 75
DETERMINE_BARCODE_ALLOWLIST 60s 1.1 GB 50
DETERMINE_BARCODE_ALLOWLIST 59s 1.1 GB 25
DETERMINE_BARCODE_ALLOWLIST 41.1s 996.7 MB 10
DETERMINE_BARCODE_MERGES 34.3s 658 MB 100
DETERMINE_BARCODE_MERGES 9.9s 570.5 MB 75
DETERMINE_BARCODE_MERGES 9.7s 369.7 MB 50
DETERMINE_BARCODE_MERGES 9.1s 198.4 MB 25
DETERMINE_BARCODE_MERGES 5s 163 MB 10
FASTQC 2h 19m 22s 596.2 MB 100
FASTQC 1h 44m 49s 609.9 MB 75
FASTQC 1h 10m 15s 602.5 MB 50
FASTQC 36m 25s 577.1 MB 25
FASTQC 8m 50s 568.3 MB 10
FINAL_BAM_MERGE 57.1s 44.2 MB 100
FINAL_BAM_MERGE 59.1s 47.8 MB 75
FINAL_BAM_MERGE 58s 46.8 MB 50
FINAL_BAM_MERGE 58.9s 45.1 MB 25
FINAL_BAM_MERGE 9.9s 44.1 MB 10
FINAL_FRAG_MERGE 59s 43.3 MB 100
FINAL_FRAG_MERGE 58.7s 45.1 MB 75
FINAL_FRAG_MERGE 49.9s 8.7 MB 50
FINAL_FRAG_MERGE 24.8s 43 MB 25
FINAL_FRAG_MERGE 8.1s 55.7 MB 10
FINAL_QC_SE 59.5s 4.7 GB 100
FINAL_QC_SE 48.9s 3 GB 75
FINAL_QC_SE 39.6s 2.6 GB 50
FINAL_QC_SE 36.2s 988.2 MB 25
FINAL_QC_SE 9.8s 762.6 MB 10
FRACTION_OF_READS_IN_PEAKS 2h 2m 32s 522.3 MB 100
FRACTION_OF_READS_IN_PEAKS 1h 39m 30s 553 MB 75
FRACTION_OF_READS_IN_PEAKS 1h 15m 56s 528.1 MB 50
FRACTION_OF_READS_IN_PEAKS 45m 3s 481.4 MB 25
FRACTION_OF_READS_IN_PEAKS 20m 45s 732.7 MB 10
FRACTION_OF_READS_IN_TSS 2h 20m 34s 512.1 MB 100
FRACTION_OF_READS_IN_TSS 1h 54m 39s 548.5 MB 75
FRACTION_OF_READS_IN_TSS 1h 26m 45s 532.8 MB 50
FRACTION_OF_READS_IN_TSS 52m 11s 500.9 MB 25
FRACTION_OF_READS_IN_TSS 24m 9s 775.7 MB 10
GENERATE_REPORTS 11m 55s 8.1 GB 100
GENERATE_REPORTS 9m 32s 7.1 GB 75
GENERATE_REPORTS 6m 22s 5.9 GB 50
GENERATE_REPORTS 2m 48s 1.6 GB 25
GENERATE_REPORTS 2m 11s 4.2 GB 10
MAKE_COUNT_MATRIX 14m 41s 20 GB 100
MAKE_COUNT_MATRIX 12m 56s 18.6 GB 75
MAKE_COUNT_MATRIX 9m 37s 16.4 GB 50
MAKE_COUNT_MATRIX 6m 20s 12.9 GB 25
MAKE_COUNT_MATRIX 3m 31s 13.5 GB 10
MARK_DUPLICATES 28m 31s 48.8 GB 100
MARK_DUPLICATES 9m 1s 42.2 GB 75
MARK_DUPLICATES 9m 49s 37.6 GB 50
MARK_DUPLICATES 7m 4s 35.8 GB 25
MARK_DUPLICATES 1m 9s 31.7 GB 10
MERGE_LANES 7m 30s 65.3 MB 100
MERGE_LANES 8m 22s 53.9 MB 75
MERGE_LANES 2m 28s 40.1 MB 50
MERGE_LANES 2m 56s 41.5 MB 25
MERGE_LANES 3.7s 55.6 MB 10
MERGE_REANN_READ_COUNTS 3.9s 126.8 MB 100
MERGE_REANN_READ_COUNTS 5.9s 127 MB 75
MERGE_REANN_READ_COUNTS 5.5s 126.9 MB 50
MERGE_REANN_READ_COUNTS 6.3s 126.8 MB 25
MERGE_REANN_READ_COUNTS 5.4s 126.9 MB 10
REANNOTATE_BAM 9s 98 MB 100
REANNOTATE_BAM 9s 97.8 MB 75
REANNOTATE_BAM 9s 97.2 MB 50
REANNOTATE_BAM 9s 90.3 MB 25
REANNOTATE_BAM 9s 6.1 MB 10
REANNOTATE_FRAGMENTS 9s 998.2 MB 100
REANNOTATE_FRAGMENTS 9s 985.5 MB 75
REANNOTATE_FRAGMENTS 9s 895.8 MB 50
REANNOTATE_FRAGMENTS 9.5s 583.7 MB 25
REANNOTATE_FRAGMENTS 5s 340.7 MB 10
SEQUENCE_SATURATION 2m 5s 7.5 GB 100
SEQUENCE_SATURATION 1m 52s 6.7 GB 75
SEQUENCE_SATURATION 1m 32s 5.6 GB 50
SEQUENCE_SATURATION 1m 4s 4 GB 25
SEQUENCE_SATURATION 37.6s 2.2 GB 10
SPLIT_BAM 3m 51s 943.4 MB 100
SPLIT_BAM 3m 34s 944 MB 75
SPLIT_BAM 41.5s 933.8 MB 50
SPLIT_BAM 59.9s 924.6 MB 25
SPLIT_BAM 9.7s 798.1 MB 10
SPLIT_FASTQ 2h 9m 36s 67.1 MB 100
SPLIT_FASTQ 1h 42m 17s 64.3 MB 75
SPLIT_FASTQ 59m 57s 65.7 MB 50
SPLIT_FASTQ 28m 28s 65.6 MB 25
SPLIT_FASTQ 6m 12s 63.1 MB 10
SUMMARIZE_ALIGNMENTS 2h 54m 18s 1.3 GB 100
SUMMARIZE_ALIGNMENTS 2h 28m 1.2 GB 75
SUMMARIZE_ALIGNMENTS 1h 43m 13s 940.6 MB 50
SUMMARIZE_ALIGNMENTS 59m 45s 1.4 GB 25
SUMMARIZE_ALIGNMENTS 32m 56s 1.4 GB 10
SUMMARIZE_MIXED_SPECIES 3.1s 96.3 MB 100
SUMMARIZE_MIXED_SPECIES 2.9s 117.3 MB 75
SUMMARIZE_MIXED_SPECIES 3.1s 105.7 MB 50
SUMMARIZE_MIXED_SPECIES 3.1s 100.1 MB 25
SUMMARIZE_MIXED_SPECIES 3.8s 121.9 MB 10
TAG_BARCODES 5m 19s 14.2 GB 100
TAG_BARCODES 7m 48s 14.1 GB 75
TAG_BARCODES 4m 34s 9.7 GB 50
TAG_BARCODES 59.7s 9.5 GB 25
TAG_BARCODES 44.1s 2.1 GB 10
TI_DEAD_CONFIG 3.4s 12.6 MB 100
TI_DEAD_CONFIG 6.7s 59.8 MB 75
TI_DEAD_CONFIG 4.9s 47.9 MB 50
TI_DEAD_CONFIG 5s 54.1 MB 25
TI_DEAD_CONFIG 6.8s 55 MB 10
TSS_ENRICHMENT 4m 23s 16.4 MB 100
TSS_ENRICHMENT 4m 21s 16.4 MB 75
TSS_ENRICHMENT 4m 19s 16.5 MB 50
TSS_ENRICHMENT 4m 17s 16.3 MB 25
TSS_ENRICHMENT 4m 15s 16.3 MB 10